Networked films of monolayer-protected clusters (MPCs), alkanethiolate-stabilized gold nanoparticles, can be thermally decomposed to form stable gold on glass substrates that are subsequently modified with self-assembled monolayers (SAMs) for use as modified electrodes. Electrochemical assessment of these SAM-modified gold substrates, including double-layer capacitance measurements, linear sweep desorption of the alkanethiolates, and diffusional redox probing, all show that SAMs formed on gold supports formed from thermolysis of MPC films possess substantially higher defect density compared to SAMs formed on traditional evaporated gold. The density of defects in the SAMs on thermolyzed gold is directly related to the strategies used to assemble the MPC film prior to thermolysis. Specifically, gold substrates formed from thermally decomposing MPC films formed with electrostatic bridges between carboxylic acid-modified MPCs and metal ion linkers are particularly sensitive to the degree of metal exposure during the assembly process. While specific metal dependence was observed, metal concentration within the MPC precursor film was determined to be a more significant factor. Specific MPC film linking strategies and pretreatment methods that emphasized lower metal exposure resulted in gold films that supported SAMs of lower defect density. The defect density of a SAM-modified electrode is shown to be critical in certain electrochemical experiments such as protein monolayer electrochemistry of adsorbed cytochrome c. While the thermal decomposition of nanoparticle film assemblies remains a viable and interesting technique for coating both flat and irregular shaped substrates, this study provides electrochemical assessment tools and tactics for determining and controlling SAM defect density on this type of gold structure, a property critical to their effective use in subsequent electrochemical applications.